Biology subjects

Ladd, D.

Publications and source records attributed to Ladd, D..

3 recordsLinked to original sources

bioRxiv2024

nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework

Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data with sequencing errors and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls, including a mixture of bulk and single-cell sequencing datasets. Using this dataset, we extended the convergence findings to 20 additional subjects, highlighting the applicability of nf-core/airrflow to validate findings in small in-house cohorts with reanalysis of large publicly available AIRR datasets. Availability and implementationnf-core/airrflow is available free of charge, under the MIT license on GitHub (https://github.com/nf-core/airrflow). Detailed documentation and example results are available on the nf-core website at (https://nf-co.re/airrflow). Visual abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/576147v2_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@e39504org.highwire.dtl.DTLVardef@14c52aforg.highwire.dtl.DTLVardef@1c87664org.highwire.dtl.DTLVardef@1d4d78b_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2020

Ca2+ release via IP3Rs increases RyR mediated Ca2+ spark frequency in ventricular cardiomyocytes without altering spark amplitude and duration

Calcium (Ca2+) plays a critical role in the excitation contraction coupling (ECC) process that governs the contraction of cardiomyocytes during each heartbeat. While ryanodine receptors (RyRs) are the primary Ca2+ channels responsible for mediating cell-wide Ca2+ transients during ECC, Ca2+ release via inositol 1,4,5-trisphosphate (IP3) receptors (IP3Rs) have been reported to elicit ECC-modulating effects. Recent studies suggest that the proximal localization of IP3Rs at dyads grants their ability to modify the occurrence of Ca2+ sparks (elementary Ca2+ release events that constitute ECC-associated Ca2+ transients) which may underlie the modulatory effects on ECC. Here, we aim to uncover the mechanism by which IP3Rs affect Ca2+ spark dynamics. To this end, we developed a mathematical model of the dyad that incorporates IP3Rs to reveal their impact on local Ca2+ handling and corresponding Ca2+ spark formation. Consistent with published experimental data, our model predicts that the propensity for Ca2+ spark formation increases with IP3R activity. Our simulations support the hypothesis that IP3R activity elevates Ca2+ within the dyad, sensitizing proximal RyRs for future release. However, this lowers Ca2+ in the JSR available for release and thus results in Ca2+ sparks with the same duration but lower amplitudes.

biophysics↗

bioRxiv2019

Detecting RyR clusters with CaCLEAN: influence of spatial distribution and structural heterogeneity

In cardiomyocytes, the coordinated release of calcium ions from intracellular stores through ryanodine receptor (RyR) clusters is key to the generation of a calcium transient and induction of contraction. Recently, a deconvolution algorithm from radio astronomy was adapted and applied to analysis of calcium fluorescence imaging of cardiomyocytes. The algorithm, CaCLEAN, showed potential in revealing both the spatial locations of RyR clusters and their functional response in living cells. However, whether the RyR clusters identified by CaCLEAN analysis of the imaging data were true or false positives remained unvalidated in the absence of ground truth values. In this work, a structurally realistic finite element model was developed to simulate reaction-diffusion of calcium emanating from RyR clusters during the rising phase (first 30 ms) of the calcium transient. The effect of two sets of factors were examined with the model: (1) the number and spacing of simulated RyR clusters and (2) the effect of mitochondria acting as barriers to diffusion. Confocal fluorescence microscopy images were simulated from the model results and analysed using CaCLEAN. The performance of CaCLEAN was found to be sensitive to cluster spacing and distance from the imaging plane. In a case with sparsely-packed clusters, detection recall and precision were 0.82 for clusters up to 610 nm from the imaging plane; in a densely-packed cluster case, recall and precision were 0.69 for clusters up to 280 nm from the imaging plane. Users interested in applying CaCLEAN to their data should therefore consider the likely density of cluster distributions and the trade-off between precision and recall when determining the maximum relevant depth of RyR clusters in their application.

bioengineering↗